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apcamargo / ictv-mmseqs2-protein-database

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can't finish the step of "taxonkit create-dump" #1

Closed lonestarling closed 2 years ago

lonestarling commented 2 years ago

Apcamargo Hi, A excellent tools for virus taxonomy, i just try your script ,but i meet a trouble about the taxonkit create-taxdump -K 1 -P 3 -C 5 -O 7 -F 9 -G 11 -S 13 -T 15 \ --rank-names "realm","kingdom","phylum","class","order","family","genus","species" \ ictv.taxonomy.tsv --out-dir ictv-taxdump

./fix_taxdump.py

i meet the error "Error: unknown shorthand flag: 'K' in -K" shoul i change the command to " taxonkit reformat -f"?, how can i solve it, sir?

Best wishes Lonestarling

apcamargo commented 2 years ago

This was probably caused by some changes in the latest version of taxonkit. Try to run it with version 0.11.1. I'll update the guide to work with version 0.12.0 in the future.

lonestarling commented 2 years ago

@apcamargo Thank you so much, sir, I will try it again.

lonestarling commented 2 years ago

Apcamargo Hi i am here again, first of all, i refer the step of mmseqs taxonomy and your script, i finally get my virus sequence annotation. but i have another question about the inputfile, i tried two options, the one is The nucleic acid sequence of the virus contig, and another is amino sequence of the virus, both of them were by mmseqs easy-taonomy. So what do I choose the two different results? General speaking, the information about annotation were generated by protein sequence blast usually. so can you give me some advice? appreciated it L

lonestarling commented 2 years ago

oh！ i get the illustration in mmseq user gude，Apcamargo

“For nucleotide-protein searches (contig taxonomy assignment) the final output is generated by the aggregatetax module, and therefore more context is provided:”

thank you so much best wishes L

apcamargo commented 2 years ago

Good to know that everything worked out, @lonestarling. I'll close this issue for now